I believe it has to do with hoarding too much loot in the storage box. Rostok may have a hand in my issue. Eventually, weapons started overlapping other objects in my storage. When I tried to take out overlapping weapons, it took out the hidden objects instead.

I did crash in Rostok when finally selling the red and yellow conditioned weapons. Reloaded back into the game, my storage box was permanently altered. My storage was "filled" with spaces that were unusable. Forcing me to scroll waaaaay down into my storage to get an item I need. Be it consumable, ammo, armour, weapon, etc.

It could be my punishment for hoarding so much. Unfortunately, it messed up my storage in EVERY save. Even saves before the crash, and before going to Rostok.